I realise there's no reason they have to, but how hard would it be for IDW to stay in continuity with the novels ?
Pretty hard, actually. Books take a lot longer to develop, write, and publish than comics, so it would be difficult for the two to stay current with each other on an ongoing basis. It's the same reason the TV shows couldn't pay much attention to the novels, because they came out so much faster and they couldn't wait around to see what happened in the books -- and the same reason that despite their best efforts, a number of books ended up getting contradicted by new episodes before they even hit the shelves. Comics don't come out at quite the same pace as TV shows, but it's sufficiently faster than novels that the same coordination problems arise.
Also IDW is in California and Pocket is in New York, so they can't coordinate as closely as they could if they were in the same place (granted, less of an issue in the age of e-mail and teleconferencing, but apparently still a factor).
Not to mention that they're targeted at different audiences. There's some overlap, certainly, but there are plenty of people who buy comics but not novels, or vice-versa. So if their continuities were dependent on each other, it might confuse people who only read one or the other. And the different media have different strengths and emphases as well. Comics rely more on action and spectacle, so they're probably better served by, for instance, keeping the Borg around as a perennial threat than by going along with their final defeat in the novels.